Study of the first nucleation steps of thin films by XPS inelastic peak shape analysis

The initial steps in the formation of thin films have been investigated by analysis of the peak shape (both inelastic background and elastic contributions) of X‐ray photoelectron spectra. Surface coverage and averaged height of the deposited particles have been estimated for several overlayers (nanometre range) after successive deposition cycles. This study has permitted the assessment of the type of nucleation and growth mechanisms of the films. The experiments have been carried out in situ in the preparation chamber of an XPS spectrometer. To check the performance of the method, several materials (i.e. cerium oxide, vanadium oxide and cadmium sulfide) have been deposited on different substrates using a variety of preparation procedures (i.e. thermal evaporation, ion beam assisted deposition and plasma enhanced chemical vapour deposition). It is shown that the first deposited nuclei of the films are usually formed by three‐dimensional particles whose heights and degree of surface coverage depend on the chemical characteristics of the growing thin film and substrate materials, as well as the deposition procedure. It is concluded that XPS peak shape analysis can be satisfactorily used as a general method to characterize morphologically the first nanometric moieties that nucleate a thin film. Copyright © 2006 John Wiley & Sons, Ltd.     

Measurement of resistant starch by enzymatic digestion in starch and selected plant materials: collaborative study

Interlaboratory performance statistics was determined for a method developed to measure the resistant starch (RS) content of selected plant food products and a range of commercial starch samples. Food materials examined contained RS (cooked kidney beans, green banana, and corn flakes) and commercial starches, most of which naturally contain, or were processed to yield, elevated RS levels. The method evaluated was optimized to yield RS values in agreement with those reported for in vivo studies. Thirty-seven laboratories tested 8 pairs of blind duplicate starch or plant material samples with RS values between 0.6 (regular maize starch) and 64% (fresh weight basis). For matrixes excluding regular maize starch, repeatability relative standard deviation (RSDr) values ranged from 1.97 to 4.2%, and reproducibility relative standard deviation (RSDR) values ranged from 4.58 to 10.9%. The range of applicability of the test is 2-64% RS. The method is not suitable for products with <1% RS (e.g., regular maize starch; 0.6% RS). For such products, RSDr and RSDR values are unacceptably high.     

Fractionation of metals and metalloids by chemical bonding from particles accumulated by electrostatic precipitation in an Argentine thermal power plant

A study was undertaken to evaluate the distribution of Al, As, Cr, Cu, Fe, Mn, Ni, Pb, Ti, V and Zn in fly ashes collected in the electrostatic precipitator of a thermal power plant in San Nicolás (Argentina). Five samples were collected during one week of operation. For the fractionation, the scheme applied consisted in extracting the elements in four fractions namely (i) soluble and exchangeable elements; (ii) carbonates, oxides and reducible elements; (iii) bound to sulfidic metals; and (iv) residual elements. Metals and metalloids at μg g^− 1 level were determined in each fraction by inductively coupled plasma optical emission spectrometry (ICP OES). For validation, a standard reference material (SRM 1633 coal fly ash) from NIST was subjected to the same chemical sequential extraction procedure that the samples. X-ray diffraction powder (XRD) analysis and scanning electron microscopy (SEM) were used to characterize the major minerals present in the matrix. Total analyte concentration (in μg g^− 1) varied from 10.6 for Pb to 17,622 for Al. Minimum and maximum concentrations (in μg g^− 1) found in individual samples in the four fractions were: Al, 92.7–9668; As, < 0.3–143; Cr, 2.0–10.4; Cu, < 0.2–35.6; Fe, < 0.3–4992; Mn, < 0.1–128; Ni, < 0.3–139; Pb, < 0.5–9.1; Ti, < 0.3–2243; V, 17.0–112.9; and Zn, < 0.1–68.2. The leachability of the 11 elements under study proved to be different. Low percentages of Al (1%), V (7%) and Cr (8%) were detected in the most bioavailable fraction. Arsenic was found to be most abundant in the non-silicate phase, represented by the second and third fractions, while Cr, Fe, Ni, Pb and Zn were mostly associated to the residual fraction.     

Trapping H- bound to the nitrogenase FeMo-cofactor active site during H2 evolution: characterization by ENDOR spectroscopy

We here show that the iron-molybdenum (FeMo)-cofactor of the nitrogenase alpha-70(Ile) molybdenum-iron (MoFe) protein variant accumulates a novel S = (1)/(2) state that can be trapped during the reduction of protons to H(2). (1,2)H-ENDOR measurements disclose the presence of two protons/hydrides (H(+/)(-)) whose hyperfine tensors have been determined from two-dimensional field-frequency (1)H ENDOR plots. The two H(+/)(-) have large isotropic hyperfine couplings, A(iso)( )() approximately 23 MHz, which shows they are bound to the cofactor. The favored analysis for these plots indicates that the two H(+/)(-) have the same principal values, which indicates that they are chemically equivalent. The tensors are further related to each other by a permutation of the tensor components, which indicates an underlying symmetry of binding relative to the cofactor. At present, no model for the structure of the iron-molybdenum (FeMo)-cofactor in the S = (1)/(2) state trapped during the reduction of H(+) can be shown unequivocally to satisfy all of the constraints generated by the ENDOR analysis. The data disfavors any model that involves protonation of sulfides, and thus suggests that the intermediate instead contains two chemically equivalent bound hydrides; it appears unlikely that these are terminal monohydrides.     

Static and dynamic light-scattering studies on micellar solutions of alkyldimethylbenzylammonium chlorides

Static (SLS) and dynamic (DLS) light-scattering techniques were applied to the study of the aggregation of dodecyl- (C12DBACl), tetradecyl- (C14DBACl), and hexadecyldimethylbenzylammonium (C16DBACl) chlorides in water and in 0.01 and 0.05 m NaCl aqueous solutions at 25 degrees C. Results of SLS measurements yielded critical micelle concentration (cmc) values for aqueous and NaCl solutions. The aggregation numbers of the micelles for the homologous surfactants are low but increase with chain length and ionic strength of the solution. Various patterns of changes of the diffusion coefficient, D, as a function of chain length, molality, and with ionic strength were found for the studied surfactants. Transformations in the structure of micelles of C14DBACl in 0.01 m NaCl occur at a concentration of surfactant of about 0.01 m. Such transformations, presumably due to rodlike structure, are the more extensive the higher the concentration of NaCl. The concentration of C16DBACl in 0.05 m NaCl covers the range where already repulsive interactions between micelles occur, as judged by the strongly negative slope of the D versus molality plot. To provide additional information on the suggested transformations, complementary viscosity measurements for C14DBACl in 0.01 m of NaCl have been performed.     

pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols

The accuracy of biological simulations depends, in large part, on the treatment of electrostatics. Due to the availability of accurate experimental values, calculation of pKa provides stringent evaluation of computational methods. The generalized solvent boundary potential (GSBP) and Ewald summation electrostatic treatments were recently implemented for combined quantum mechanical and molecular mechanics (QM/MM) simulations by our group. These approaches were tested by calculating pKa shifts due to differences in electronic structure and electrostatic environment; the shifts were determined for a series of small molecules in solution, using various electrostatic treatments, and two residues (His 31, Lys 102) in the M102K T4-lysozyme mutant with large pKa shifts, using the GSBP approach. The calculations utilized a free energy perturbation scheme with the QM/MM potential function involving the self-consistent charge density functional tight binding (SCC-DFTB) and CHARMM as the QM and MM methods, respectively. The study of small molecules demonstrated that inconsistent electrostatic models produced results that were difficult to correct in a robust manner; by contrast, extended electrostatics, GSBP, and Ewald simulations produced consistent results once a bulk solvation contribution was carefully chosen. In addition to the electrostatic treatment, the pKa shifts were also sensitive to the level of the QM method and the scheme of treating QM/MM Coulombic interactions; however, simple perturbative corrections based on SCC-DFTB/CHARMM trajectories and higher level single point energy calculations were found to give satisfactory results. Combining all factors gave a root-mean-square difference of 0.7 pKa units for the relative pKa values of the small molecules compared to experiment. For the residues in the lysozyme, an accurate pKa shift was obtained for His 31 with multiple nanosecond simulations. For Lys 102, however, the pKa shift was estimated to be too large, even after more than 10 nanosecond simulations for each lambda window; the difficulty was due to the significant, but slow, reorganization of the protein and water structure when Lys 102 was protonated. The simulations support that Lys 102 is deprotonated in the X-ray structure and the protein is highly destabilized when this residue is protonated.     

Computational studies of the 3-Dimensional structure of cyclopenta polycyclic aromatic hydrocarbons containing a gulf region

Recently, some cyclopenta-fused polyaromatic hydrocarbons, an environmentally relevant subclass of chemicals, have been shown to have carcinogenic activity in animals. It has been suggested that benz[l] aceanthrylene ( I ), an active member of this subclass with a gulf region, has a trans dihydrodiol metabolite that is nonplanar and has two distinct spatial configurations. We have used MMP 2(85) and AM 1 to investigate the three-dimensional structure of this dihydrodiol and other similar derivatives of ( I ) and have found that although ( I ) is somewhat nonplanar the relevant derivatives are all nearly planar. Further, we have computed potential functions for the bending of the angular ring in the gulf region using MMP 2(85), AM 1, and ab initio computed energies for AM 1 spatial configurations and find that these molecules all have only a single potential minimum. We have performed the same calculations for benzo[c]phenanthren and its 1,12 dimethyl derivative, molecules with a similar gulf region for which crystallographic data exists. In agreement with that data, we find that two distinct spatial configurations exist separated by significant barries. The differences between the results generated by the three different methods of computation will be discussed.     

Occurrence of Neighboring Group Participation Reactions in Amide-N and Amidine Complexes Derived from Pentaammine(dinitrile)cobalt(III) Ions

N-Bonded pentaamminecobalt(III) complexes of 2-cyanobenzamide, 2-cyanoacetamide, and fumaric, succinic, glutaric, and adipic amide-nitriles have been prepared. The kinetics of the base hydrolysis of (succinonitrile)pentaamminecobalt(III) have been measured: k(obsd) = k(OH) [OH(-)]; k(OH) = 1.23 x 10(3) {I = 1.00 M (NaCH(3)COO), 25 degrees C}. Amido-N-coordinated 2-cyanobenzamide cyclized in aqueous base, and it forms [(1-oxo-3-iminoisoindolino-endo-N)pentaamminecobalt(III). In aqueous acid it protonates on the exo-imine and solvolyzes (k(H) = 7.9 x 10(-)(5) s(-)(1)), forming the pentaammineaquacobalt(III) complex and 1-oxo-3-iminoisoindoline. In aqueous acid the amido-N complexes are protonated on the amide oxygen. The 2-cyanobenzamide species rearranges to form the nitrile-bonded linkage isomer in aqueous acid and also in Me(2)SO-d(6), while the succinic amide nitrile complex rearranges more slowly in aqueous acid to form solely the nitrile-bonded linkage isomer. The kinetics of the reaction were k(obsd) = f(k(H)[H(+)]/(K(a) + [H(+)])) where k(H) = 3.4 x 10(-)(4) M(-)(1) s(-)(1) and K(a) = 6.76 x 10(-)(2) M, pK(a) 1.2; pK(a) 1.3 (spectrophotometric) {I = 1.00 M (LiClO(4).3H(2)O), 25 degrees C}. In Me(2)SO-d(6) this amide-N complex reacts by three pathways: solvolysis, amide-N to -O isomerization, and amide-N to nitrile-bonded rearrangement (10%). The conjugate acid of the 2-cyanoacetamido-N complex reacted in both aqueous acid and acidified Me(2)SO-d(6) by solvolysis, amide N to O isomerization, and amide-N to nitrile-bonded rearrangement (17% in each solvent). The fumaric, glutaric, and adipic amide-nitrile complexes bonded through the amide nitrogen react only by solvolysis and amide-N to -O isomerization. Pentaamminecobalt(III) complexes of 2-cyanobenzamidine and succinic, glutaric, and adipic amidine-nitriles bonded through the amidine secondary nitrogen have been prepared. The 2-cyanobenzamidine complex undergoes rapid ligand cyclization to form the corresponding complex of 1,3-diiminoisoindoline bonded through the deprotonated endocyclic nitrogen. In aqueous acid the complex is protonated on one of the exo-imines, and this solvolyzes to form the pentaammineaquacobalt(III) complex and 1,3-diiminoisoindoline {k(H) = 1.7 x 10(-)(3) s(-)(1) (0.5 M HCl, 25 degrees C). Coordinated succinic amidine-nitrile also cyclizes in liquid ammonia to yield the complex of 2,5-diiminopyrrolidine bonded through the deprotonated endocyclic nitrogen. This is stable in aqueous base but solvolyzes rapidly (t(1/2) (s)) in aqueous acid to the aqua complex and succinimide; the latter is formed by hydrolysis of the free 2,5-diiminopyrrolidine. The dinuclear complex &mgr;-decaammine(succinonitrile)dicobalt(III) was synthesized; in aqueous base it forms &mgr;-(succinamido-N)decaamminecobalt(III). The dinuclear dinitrile complex reacts in liquid ammonia to form the corresponding succinic amidine-nitrile species which cyclizes rapidly to form &mgr;-decaammine(2,5-diiminopyrrolidino)cobalt(III) in which the ligand is bonded to cobalt(III) through the exo-imines.     

Global and local electrophilicity patterns of diazonium ions and their reactivity toward pi-nucleophiles

The global and local electrophilicity patterns of a series of 15 diazonium ions have been evaluated using the absolute scale of electrophilicity proposed by Parr et al. (J. Am. Chem. Soc. 1999, 121, 1922). The predicted global electrophilicity pattern of the whole series of diazonium ions correctly compares with the experimental electrophilicity recently determined for these charged electrophiles. The global electrophilicity is then projected into the different potential active sites of the molecular ions using the electrophilic Fukui function. The highest regional electrophilicity power is found at the terminal nitrogen atom of the arenediazonium ions, yet the highest positive charge is located on the nitrogen atom directly attached to the aromatic ring. This result is consistent with the observed reactivity displayed by diazonium ions toward substituted alkenes, thereby suggesting that the formation of the azocarbocation intermediate is mostly orbital rather than charge controlled.     

Molecular nitrides containing group 4 and 5 metals: single and double azatitanocubanes

Treatment of [[Ti(eta(5)-C(5)Me(5))(micro-NH)](3)(micro(3)-N)] (1) with the imido complexes [Ti(NAr)Cl(2)(py)(3)] (Ar=2,4,6-C(6)H(2)Me(3)) and [Ti(NtBu)Cl(2)(py)(3)] in toluene affords the single azatitanocubanes [[Cl(2)(ArN)Ti]( micro(3)-NH)(3)[Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)]].(C(7)H(8)) (2.C(7)H(8)) and [[Cl(2)Ti](micro(3)-N)(2)(micro(3)-NH)[Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)]] (3), respectively. Similar reactions of complex 1 with the niobium and tantalum imido derivatives [[M(NtBu)(NHtBu)Cl(2)(NH(2)tBu)](2)] (M=Nb, Ta) in toluene give the single azaheterometallocubanes [[Cl(2)(tBuN)M](micro(3)-N)(micro(3)-NH)(2)[Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)]] (M=Nb (4), Ta (5)), both complexes react with 2,4,6-trimethylaniline to yield the analogous species [[Cl(2)(ArN)M](micro(3)-N)(micro(3)-NH)(2)[Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)]].(C(7)H(8)) (Ar=2,4,6-C(6)H(2)Me(3), M=Nb (6.C(7)H(8)), Ta (7.C(7)H(8))). Also the azaheterodicubanes [M[micro(3)-N)(2)(micro(3)-NH)](2)[Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)](2)].2C(7)H(8) [M=Ti (8.2C(7)H(8)), Zr (9.2C(7)H(8))], and [M[(micro(3)-N)(5)(micro(3)-NH)][Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)](2)].2 C(7)H(8) (Nb (10.2C(7)H(8)), Ta (11.2C(7)H(8))) were prepared from 1 and the homoleptic dimethylamido complex [M(NMe(2))(x)] (x=4, M=Ti, Zr; x=5, M=Nb, Ta) in toluene at 150 degrees C. X-ray crystal structure determinations were performed for 6 and 10, which revealed a cube- and double-cube-type core, respectively. For complexes 2 and 4-7 we observed and studied by DNMR a rotation or trigonal-twist of the organometallic ligands [[Ti(eta(5)-C(5)Me(5))(micro-NH)](3)(micro(3)-N)] (1) and [(micro(3)-N)(micro(3)-NH)(2)[Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)]](1-). Density functional theory calculations were carried out on model complexes of 2, 3, and 8 to establish and understand their structures.